Simultaneous multithreading is a technique that can improve performance when running parallel applications on the Intel Xeon Phi co-processor. Selecting the most efficient thread count is however non-trivial, as the potential increase in efficiency has to be balanced against other, potentially negative factors such as inter-thread competition for cache capacity and increased synchronization overheads. In this paper, we extend CRUST (ClusteR-aware Under-subscribed Scheduling of Threads), a technique for finding the optimum thread count of OpenMP applications running on clustered cache architectures, to take the behavior of simultaneous multithreading on the Xeon Phi into account. CRUST can automatically find the optimum thread count at sub-application granularity by exploiting application phase behavior at OpenMP parallel section boundaries, and uses hardware performance counter information to gain insight into the application's behavior. We implement a CRUST prototype inside the Intel OpenMP runtime library and show its efficiency running on real Xeon Phi hardware.